If you have a single-stranded RNA that is complementary to a double-stranded DNA, how do they interact to form what my prof. calls a "triplex structure"?



I don't understand how the DNA can form 2 bonds there?

  • $\begingroup$ None of those sequences are RNA. I assume it's the one at the top that is supposed to be? $\endgroup$ – Alan Boyd Nov 24 '12 at 7:57
  • $\begingroup$ Sorry I fixed that, yes the one on top is RNA $\endgroup$ – Jon Shaulfer Nov 24 '12 at 10:58

DNA-RNA triplex formation is well-documented. It was originally analysed in simple model polynucleotides where the DNA has a polypurine strand and the RNA has a polypyrimidine, e.g.



but it is now known to occur in more complex sequences. One of the best studied examples is in the promoter of the human DHFR gene:

Gee, J. E. et al.(1992) Triplex formation prevents Sp1 binding to the dihydrofolate reductase promoter. J. Biol. Chem. 267, 11163–11167

enter image description here

In this work the oligonucleotide GR19 was shown to bind in a triple helix to SpI binding site I in the DHFR promoter (CR19 was used as a control). Triplex formation was detected by gel shift, and the specificity was confirmed by DNase I footprinting.

This effect is part of the regulation of DHFR - the transcript from a minor upstream promoter binds to the major promoter, see:

Martianov, I. et al. (2007) Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445: 666-670

The structure of these triple helices involves a combination of Watson-Crick base pairing in the DNA duplex together with Hoogsteen base pairing in the RNA-DNA interaction:

enter image description here

Figure taken from:

Morgan, A. R. & Wells, R. D. (1968) Specificity of the three-stranded complex formation between double-stranded DNA and single-stranded RNA containing repeating nucleotide sequences. J. Mol. Biol. 37, 63–80


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